Contacts of the strand formed by residues 128 - 138 (chain A) in PDB entry 1KP5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PRO* 3.4 28.6 - - + +
24A ILE 4.2 0.7 - - - -
25A LEU* 3.6 32.1 - - + +
124A PHE* 3.4 4.1 - - - -
125A GLU 2.9 38.8 + - - +
126A GLY 3.3 0.4 - - - -
127A ASP* 1.3 80.2 - - - +
129A LEU* 1.3 66.1 + - - +
130A VAL* 3.4 6.7 + - + +
359B THR 4.1 4.5 + - - +
360B THR* 3.5 29.5 + - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.5 1.1 - - + -
22A VAL* 4.2 6.6 - - + +
23A PRO 2.9 12.0 + - - +
24A ILE* 3.4 5.0 - - + +
25A LEU 3.0 23.2 + - - +
78A VAL* 3.6 32.1 - - + -
80A CYS* 4.0 11.0 - - - -
81A PHE* 3.7 32.5 - - + -
98A MET* 4.1 13.0 - - + -
122A VAL* 3.6 22.4 - - + -
123A LYS 3.8 18.2 - - - +
124A PHE* 4.2 14.3 - - + -
127A ASP 4.1 0.8 + - - -
128A THR* 1.3 69.8 - - - +
130A VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.4 26.2 - - + +
27A GLU* 5.5 0.2 - - + -
121A GLU 3.4 2.4 - - - +
122A VAL* 3.1 5.5 - - - +
123A LYS* 2.8 40.0 + - + +
125A GLU* 3.7 41.5 - - + +
128A THR* 3.7 21.1 - - + +
129A LEU* 1.3 79.9 - - - +
131A ASN* 1.3 69.3 - - - +
132A ARG* 3.9 16.4 - - + +
360B THR* 3.9 8.1 - - + -
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Residues in contact with ASN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU 3.0 10.5 + - - +
26A VAL* 3.4 9.0 - - + -
27A GLU 3.0 24.9 + - - +
73A THR 3.3 13.2 + - - +
74A PHE 2.8 23.0 - - - +
76A GYS 3.5 13.5 + - - +
78A VAL* 3.8 18.6 - - + -
120A ALA* 3.6 10.1 - - - +
121A GLU 3.5 1.3 + - - -
122A VAL* 3.5 18.6 - - + +
129A LEU 4.2 0.2 + - - -
130A VAL* 1.3 74.0 - - - +
132A ARG* 1.3 61.9 + - - +
133A ILE* 3.5 21.4 - - - +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.2 35.6 - - + +
120A ALA* 3.2 2.9 - - - +
121A GLU* 2.9 40.4 + - + +
125A GLU* 4.4 7.0 + - - +
130A VAL* 3.9 13.2 - - + +
131A ASN* 1.3 74.0 - - - +
133A ILE* 1.3 64.9 + - - +
134A GLU* 6.4 0.7 - - + -
327B GLU* 5.1 6.9 + - - +
328B LEU 4.8 3.8 + - - -
329B ASP* 3.4 46.0 + - - +
338B SER* 3.1 35.2 + - - -
432B ARG* 5.1 10.0 - - - +
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.9 13.0 - - + -
27A GLU 2.8 20.1 + - - +
28A LEU* 3.4 29.1 - - + -
29A ASP* 2.9 25.9 + - - +
73A THR* 3.7 26.7 - - + +
74A PHE* 4.7 1.1 - - - -
118A THR* 4.2 8.5 - - + -
119A ARG 3.5 11.7 - - - +
120A ALA* 3.5 16.6 - - + -
131A ASN* 3.5 30.5 - - - +
132A ARG* 1.3 80.7 - - - +
134A GLU* 1.3 78.4 + - - +
135A LEU 4.1 0.4 - - - +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ASP* 3.4 17.1 - - + +
117A LYS 3.9 0.5 - - - +
118A THR* 3.5 3.1 - - - -
119A ARG* 3.0 48.2 + - + +
132A ARG* 6.4 0.9 - - + -
133A ILE* 1.3 78.2 - - - +
135A LEU* 1.3 60.3 + - - +
432B ARG* 6.0 1.7 - - - -
924B SO4 4.8 12.0 + - - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.9 25.6 - - + -
29A ASP 2.8 11.8 + - - +
30A GLY* 3.2 6.7 - - - -
31A ASP* 3.0 26.7 + - - +
32A VAL* 3.8 24.7 - - + -
37A PHE* 4.7 3.4 - - + -
70A LEU* 4.0 27.4 - - + -
73A THR* 4.4 5.6 - - + +
116A TYR* 4.2 16.6 - - + -
117A LYS 3.5 2.7 - - - +
118A THR* 3.6 24.0 - - + -
133A ILE 4.1 0.2 - - - -
134A GLU* 1.3 75.0 - - - +
136A LYS* 1.3 77.7 + - - +
137A GLY 3.9 0.2 - - - +
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASP* 3.3 29.9 + - + +
34A GLY 5.9 0.2 - - - +
115A ASN* 3.9 1.0 - - - +
117A LYS* 2.7 51.4 + - + +
135A LEU* 1.3 79.3 - - - +
137A GLY* 1.3 58.5 + - - +
138A ILE* 4.1 25.4 - - + +
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP 2.8 11.7 + - - +
32A VAL* 3.5 4.6 - - - -
33A ASN 3.0 24.9 + - - -
115A ASN 3.1 11.4 - - - -
116A TYR* 4.1 8.7 - - - -
135A LEU* 3.9 2.8 - - - +
136A LYS* 1.3 75.1 + - - +
138A ILE* 1.3 68.8 + - - +
140A PHE* 4.0 12.3 - - - -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.4 8.7 - - - +
114A GLY* 3.2 9.7 - - - -
115A ASN* 3.1 26.8 + - - +
117A LYS* 6.1 3.4 - - - -
136A LYS* 4.1 30.1 - - + +
137A GLY* 1.3 79.8 - - - +
139A ASP* 1.3 88.0 + - - +
140A PHE* 3.1 14.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il